Developing Ontologies and more

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Developing Ontologies(and more)

• Peter Fox (NCAR)
• ESIP Winter Meeting (TIWG)
• January 9, 2008, Washington, D.C.

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Ontology Spectrum
Thesauri narrower term relation
Selected Logical Constraints (disjointness,
inverse, )
Frames (properties)
Formal is-a
Catalog/ ID
Informal is-a
Formal instance
General Logical constraints
Terms/ glossary
Value Restrs.
Originally from AAAI 1999- Ontologies Panel by
Gruninger, Lehmann, McGuinness, Uschold, Welty
updated by McGuinness. Description in
www.ksl.stanford.edu/people/dlm/papers/ontologies-
come-of-age-abstract.html
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Ontology - declarative knowledge

• The triple subject-predicate-object
• interferometer is-a optical instrument
• Fabry-Perot is-a interferometer
• Optical instrument has focal length
• Optical instrument is-a instrument
• Instrument has instrument operating mode
• Data archive has measured parameter
• SO2 concentration is-a concentration
• Concentration is-a parameter

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Semantic Web Layers
http//www.w3.org/2003/Talks/1023-iswc-tbl/slide26
-0.html, http//flickr.com/photos/pshab/291147522/
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Terminology

• Ontology (n.d.). The Free On-line Dictionary of
  Computing. http//dictionary.reference.com/browse/
  ontology
• An explicit?formal specification of how to
  represent the objects, concepts?and other
  entities that are assumed to exist in some area
  of?interest and the relationships that hold among
  them.
• Semantic Web
• An extension of the current web in which
  information is given well-defined meaning, better
  enabling computers and people to work in
  cooperation, www.semanticweb.org
• Primer http//www.ics.forth.gr/isl/swprimer/
• Languages
• OWL 1.0 (Lite, DL, Full) - Web Ontology Language
  (W3C)
• RDF - Resource Description Framework (W3C)
• OWL-S/SWSL - Web Services (W3C)
• WSMO/WSML - Web Services (EC/W3C)
• SWRL - Semantic Web Rule Language, RIF- Rules
  Interchange Format
• Editors Protégé, SWOOP, CoE, VOM, Medius, SWeDE,
  

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OWL and RDF

• OWL
• Lite
• DL
• Full
• RDF
• Services
• OWL-S
• SWSL
• WSML
• SAWSDL - (WSDL-S)
• Rules
• SWRL

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Developing Ontologies

• Approach
• Bottom-up
• Top-down (upper-level or foundational)
• Mid-level (use case)
• Using tools
• Coding and testing
• Iterating
• Maintaining and evolving (curation, preservation)

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GRDDL - bottom up

• GRDDL - Gleaning Resource Descriptions from
  Dialects of Languages
• Pretty much XML/XHTML (for e.g.) into RDF via
  XSLT
• Good support, e.g. Jena
• Handles microformats
• Active community
• How to categorize, use, re-use (parts of)?

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Collecting

• RDFa extends XHTML by
• extending the link and meta to include child
  elements
• add metadata to any elements (a bit like the
  class in micro-formats, but via dedicated
  properties)
• It is very similar to micro-formats, but with
  more rigor
• it is a general framework (instead of an
  agreement on the meaning of, say, a class
  attribute value)
• terminologies can be mixed more easily
• ATOM (used with RSS)

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Foundational Ontologies

• CONTENTS
• General concepts and relations that apply in all
  domains
• physical object, process, event,, inheres,
  participates,
• Rigorously defined
• formal logic, philosophical principles, highly
  structured
• Examples
• DOLCE, BFO, GFO, SUMO, CYC, (Sowa)

Courtesy Boyan Brodaric
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Foundational Ontologies
PURPOSE help integrate domain ontologies
Courtesy Boyan Brodaric
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Foundational Ontologies
PURPOSE help organize domain ontologies
Courtesy Boyan Brodaric
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Problem scenario

• Little work done on linking foundational
  ontologies with geoscience ontologies
• Such linkage might benefit various scenarios
  requiring cross-disciplinary knowledge, e.g.
• water budgets groundwater (geology) and surface
  water (hydro)
• hazards risk hazard potential (geology,
  geophysics) and items at threat (infrastructure,
  people, environment, economic)
• health toxic substances (geochemistry) and
  people, wildlife
• many others

Courtesy Boyan Brodaric
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DOLCE
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DOLCE SWEET

• Benefits
• full coverage
• rich relations
• home for orphans
• single superclasses

• Issues
• individuals (e.g. Planet Earth)
• roles (contaminant)
• features (SeaFloor)

Courtesy Boyan Brodaric
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Conclusions

• Surprisingly good fit amongst ontologies
• so far no show-stopper conflicts, a few
  difficult conflicts
• DOLCE richness benefits geoscience ontologies
• good conceptual foundation helps clear some
  existing problems
• Unresolved issues in modeling science entities
• modeling classifications, interpretations,
  theories, models,

• Same procedure with GeoSciML

Courtesy Boyan Brodaric
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SUMO - Standard Upper Merged Ontology

• Physical
• Object
• SelfConnectedObject
• ContinuousObject
• CorpuscularObject
• Collection
• Process
• Abstract
• SetClass
• Relation
• Proposition
• Quantity
• Number
• PhysicalQuantity
• Attribute

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Using SNAP/ SPAN
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GeoSciOnt?
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Using SWEET

• Plug-in (import) domain detailed modules
• Lots of classes, few relations (properties)

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Mix-n-Match

• The IRI example
• Collect a lot of different ontologies
  representing different terms, levels of concepts,
  etc. into a base form RDF
• See Bennos talk in session 1b.
• MMI
• Others

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CF attributes
NC basic attributes
IRIDL attributes/objects
CF data objects
CF Standard Names (RDF object)
SWEET Ontologies (OWL)
Location
IRIDL Terms
CF Standard Names As Terms
SWEET as Terms
Search Terms
Gazetteer Terms
Blumenthal
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IRI RDF Architecture
Data Servers
MMI
Ontologies
JPL
Start Point
bibliography
Standards Organizations
RDF Crawler
Location Canonicalizer
RDFS Semantics Owl Semantics SWRL Rules SeRQL
CONSTRUCT
Time Canonicalizer
Sesame
Search Queries
Blumenthal
Search Interface
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Mid-Level Developing ontologies

• Use cases and small team (7-8 2-3 domain
  experts, 2 knowledge experts, 1 software
  engineer, 1 facilitator, 1 scribe)
• Identify classes and properties (leverage
  controlled vocab.)
• Start with narrower terms, generalize when needed
  or possible
• Adopt a suitable conceptual decomposition (e.g.
  SWEET)
• Import modules when concepts are orthogonal
• Review, vet, publish
• Only code them (in RDF or OWL) when needed (CMAP,
  )
• Ontologies small and modular

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Use Case example

• Plot the neutral temperature from the
  Millstone-Hill Fabry Perot, operating in the
  vertical mode during January 2000 as a time
  series.
• Plot the neutral temperature from the
  Millstone-Hill Fabry Perot, operating in the
  vertical mode during January 2000 as a time
  series.
• Objects
• Neutral temperature is a (temperature is a)
  parameter
• Millstone Hill is a (ground-based observatory is
  a) observatory
• Fabry-Perot is a interferometer is a optical
  instrument is a instrument
• Vertical mode is a instrument operating mode
• January 2000 is a date-time range
• Time is a independent variable/ coordinate
• Time series is a data plot is a data product

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Class and property example

• Parameter
• Has coordinates (independent variables)
• Observatory
• Operates instruments
• Instrument
• Has operating mode
• Instrument operating mode
• Has measured parameters
• Date-time interval
• Data product

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Higher level use case

• Find data which represents the state of the
  neutral atmosphere above 100km, toward the arctic
  circle at any time of high geomagnetic activity
• Find data which represents the state of the
  neutral atmosphere above 100km, toward the arctic
  circle at any time of high geomagnetic activity

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Translating the Use-Case - non-monotonic?
GeoMagneticActivity has ProxyRepresentation Geophy
sicalIndex is a ProxyRepresentation (in Realm of
Neutral Atmosphere) Kp is a GeophysicalIndex
hasTemporalDomain daily hasHighThreshold
xsd_number 8 Date/time when KP gt 8
Specification needed for query to
CEDARWEB Instrument Parameter(s) Operating
Mode Observatory Date/time Return-type data

• Input
• Physical properties State of neutral atmosphere
• Spatial
• Above 100km
• Toward arctic circle (above 45N)
• Conditions
• High geomagnetic activity
• Action Return Data

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Translating the Use-Case - ctd.
NeutralAtmosphere is a subRealm of
TerrestrialAtmosphere hasPhysicalProperties
NeutralTemperature, Neutral Wind,
etc. hasSpatialDomain 0,360,0,180,100,150 h
asTemporalDomain NeutralTemperature is a
Temperature (which) is a Parameter
Specification needed for query to
CEDARWEB Instrument Parameter(s) Operating
Mode Observatory Date/time Return-type data
Input Physical properties State of neutral
atmosphere Spatial Above 100km Toward arctic
circle (above 45N) Conditions High geomagnetic
activity Action Return Data
FabryPerotInterferometer is a Interferometer,
(which) is a Optical Instrument (which) is a
Instrument hasFilterCentralWavelength
Wavelength hasLowerBoundFormationHeight
Height ArcticCircle is a GeographicRegion hasLati
tudeBoundary hasLatitudeUpperBoundary
GeoMagneticActivity has ProxyRepresentation Geophy
sicalIndex is a ProxyRepresentation (in Realm of
Neutral Atmosphere) Kp is a GeophysicalIndex
hasTemporalDomain daily hasHighThreshold
xsd_number 8 Date/time when KP gt 8
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Tools - Using Protégé
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Creating Ontologies - visual

• UML - new release of ODM/MOF
• Ontology Definition Metamodel/Meta Object
  Facility (OMG) for UML
• Provides standardized notation
• CMAP Ontology Editor (concept mapping tool from
  IHMC)
• Drag/drop visual development of classes, subclass
  (is-a) and property relationship
• Read and writes OWL
• Formal convention (OWL/RDF tags, etc.)
• White board, text file

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Using CMAP/COE
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Is OWL the only option? No

• SKOS - Simple Knowledge Organization Scheme
• Annotations (RDFa)
• Atom
• Natural Language (read results from a web search
  and transform to a usable form)
• CL (common logic)
• Rabbit, e.g. ShellfishCourse is a Meal Course
  that (if has drink) always has drink Potable
  Liquid that has Full body and which either has
  Moderate or Strong flavour
• PENG (processable English)

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Is OWL the only option II? No

• Natural Language (NL)
• Read results from a web search and transform to a
  usable form
• Find/filter out inconsistencies,
  concepts/relations that cannot be represented
• Popular options
• CLCE (common logic controlled english)
• Rabbit, e.g. ShellfishCourse is a Meal Course
  that (if has drink) always has drink Potable
  Liquid that has Full body and which either has
  Moderate or Strong flavour
• PENG (processable English)
• Really need PSCI - process-able science

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Creating Ontologies - verbal

• Translating use cases
• E.g. Find data which represents the state of the
  neutral atmosphere above 100km, toward the arctic
  circle at any time of high geomagnetic activity
• Can this be expressed as an ontology?
• CLCE, Rabbit, PENG, Sydney syntax
• Notice something about the next examples?

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Sydney syntax

• If X has Y as a father then Y is the only father
  of X.
• The class person is equivalent to male or female,
  and male and female are mutually exclusive.
• equivalent to
• The classes male and female are mutually
  exclusive. The class person is fully defined as
  anything that is a male or a female.

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PENG - Processible English

• If X is a research programmer then X is a
  programmer.
• Bill Smith is a research programmer who works at
  the CLT.
• Who is a programmer and works at the CLT?

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CLCE - Common Logic Controlled English

• CLCE If a set x is the set of (a cat, a dog,
  and an elephant), then the cat is an element of
  x, the dog is an element of x, and the elephant
  is an element of x.
• PC(?xSet)(?x1Cat)(?x2Dog)(?x3Elephant)(Set(x
  ,x1,x2,x3) ? (x1?x ? x2?x ? x3?x))

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Use Case

• Provide a decision support capability for an
  analyst to determine an individuals
  susceptibility to avian flu without having to be
  precise in terminology (-nyms)

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Using ThManager
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Services

• Ontologies of services, provides
• What does the service provide for prospective
  clients? The answer to this question is given in
  the "profile," which is used to advertise the
  service. To capture this perspective, each
  instance of the class Service presents a
  ServiceProfile.
• How is it used? The answer to this question is
  given in the "process model." This perspective is
  captured by the ServiceModel class. Instances of
  the class Service use the property describedBy to
  refer to the service's ServiceModel.
• How does one interact with it? The answer to this
  question is given in the "grounding." A grounding
  provides the needed details about transport
  protocols. Instances of the class Service have a
  supports property referring to a ServiceGrounding.

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Developing a service ontology

• Use case find and display in the same
  projection, sea surface temperature and land
  surface temperature from a global climate model.
• Find and display in the same projection, sea
  surface temperature and land surface temperature
  from a global climate model.
• Classes/ concepts
• Temperature
• Surface (sea/ land)
• Model
• Climate
• Global
• Projection
• Display

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Service ontology

• Climate model is a model
• Model has domain
• Climate Model has component representation
• Land surface is-a component representation
• Ocean is-a component representation
• Sea surface is part of ocean
• Model has spatial representation (and temporal)
• Spatial representation has dimensions
• Latitude-longitude is a horizontal spatial
  representation
• Displaced pole is a horizontal spatial
  representation
• Ocean model has displaced pole representation
• Land surface model has latitude-longitude
  representation
• Lambert conformal is a geographic spatial
  representation
• Reprojection is a transform between spatial
  representation
• .

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Service ontology

• A sea surface model has grid representation
  displaced pole and land surface model has grid
  representation latitude-longitude and both must
  be transformed to Lambert conformal for display

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Best practices

• Ontologies/ vocabularies must be shared and
  reused - swoogle.umbc.edu, www.planetont.org
• Examine core vocabularies to start with
• SKOS Core about knowledge systems
• Dublin Core about information resources, digital
  libraries, with extensions for rights,
  permissions, digital right management
• FOAF about people and their organizations
• DOAP on the descriptions of software projects
• DOLCE seems the most promising to match science
  ontologies
• Go Lite as much as possible, then DL and only
  if you have to Full - balancing expressibility
  vs. implementability
• Minimal properties to start, add only when needed

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Tutorial Summary

• Many different options for ontology development
  and encoding
• Tools are in reasonable shape, no killer-tool
• Best practices DO exist
• PLEASE DO NOT just start coding OWL!
• Use case should drive the functional requirements
  of both your ontology and how you will build
  one
• PARTNER with someone already familiar

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More information

• OWL-S - http//www.w3.org/Submission/OWL-S
• SWSO/F/L - Semantic Web Services
  Ontology/Framework/Language - http//www.w3.org/S
  ubmission/SWSF/
• WSMO/X/L - Web Services Modeling
  Ontology/Exection/Language - http//www.w3.org/Sub
  mission/WSMX/ www.wsmo.org, www.wsmx.org
• SAWSDL - (WSDL-S)

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Other tools

• Reasoners
• Pellet, Racer, Medius KBS, FACT, fuzzyDL,
  KAON2, MSPASS, QuOnto
• Query Languages
• SPARQL, XQUERY, SeRQL, OWL-QL, RDFQuery
• Other Tools for Semantic Web
• Search SWOOGLE swoogle.umbc.edu
• Collaboration www.planetont.org
• Other Jena, SeSAME/SAIL, Mulgara, Eclipse,
  KOWARI
• Semantic wiki OntoWiki, SemanticMediaWiki

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Editors

• Protégé (http//protégé.stanford.edu)
• SWOOP (http//mindswap.org/2004/SWOOP)
• Altova SemanticWorks (http//www.altova.com/downlo
  ad/semanticworks/semantic_web_rdf_owl_editor.html)
  
• SWeDE (http//owl-eclipse.projects.semwebcentral.o
  rg/InstallSwede.html), goes with Eclipse
• Medius
• TopBraid Composer and other commercial tools
• Visual Ontology Modeler (VOM) - Sandpiper
• CMAP Ontology Editor (COE) (http//cmap.ihmc.us/co
  e)

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What about Earth Science?

• SWEET (Semantic Web for Earth and Environmental
  Terminology)
• http//sweet.jpl.nasa.gov
• based on GCMD terms
• modular using faceted and integrative concepts
• VSTO (Virtual Solar-Terrestrial Observatory)
• http//vsto.hao.ucar.edu
• captures observational data (from instruments)
• modular using domains
• MMI
• http//marinemetadata.org
• captures aspects of marine data, ocean observing
  systems
• partly modular, mostly by developed project
• GeoSciML
• http//www.opengis.net/GeoSciML/
• is a GML (Geography ML) application language for
  Geoscience
• modular, in packages